ddRAD analyses reveal a credible phylogenetic relationship of the four main genera of Bambusa-Dendrocalamus-Gigantochloa complex (Poaceae: Bambusoideae)
ddRAD analyses reveal a credible phylogenetic relationship of the four main genera of Bambusa-Dendrocalamus-Gigantochloa complex (Poaceae: Bambusoideae)
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ddRAD 分析揭示了竹 - 竹竹 - 巨竹复合体（禾本科：竹亚科）四个主要属之间可靠的系统发育关系
DOI：
10.1016/j.ympev.2020.106758
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发表时间：
2020-05-01
影响因子：
4.1
通讯作者：
Li, De-Zhu
中科院分区：
文献类型：
--
作者：
Liu, Jing-Xia;Zhou, Meng-Yuan;Li, De-Zhu
Bambusa-Dendrocalamus-Gigantocalamus复合体（BDG复合体）是古热带木本竹类中最具多样性和遗传多样性的类群。该复合体的物种分布于亚洲热带和亚热带，大多数具有重要的经济、文化和生态价值。通过对以前的分子数据集的分析所获得的分辨率的缺乏长期以来混淆了其系统发育估计和属的界定。在这里，我们采用了ddRAD-seq策略，以调查四个主要属（竹，龙竹，Gigantocalamus和Melocalamus）的BDG复合体的系统发育关系。共对102个物种进行了采样，并生成了SNP数据。ddRAD-seq数据的MP和ML分析都产生了良好解析的拓扑结构，其中Gigantoalea和Melocalamus被确认为单系，Melocalamus被解析为复合体其余部分的姐妹。竹类和龙竹类都被认为是并系起源。系统发育关系主要由形态学证据支持，包括分支补充，小穗轴，浆片，花丝和柱头的特征。我们还生成并组装了48个代表性物种的完整质体基因组。plastome和ddRAD拓扑结构之间存在冲突。我们的研究表明，RAD-seq可用于重建谱系的进化历史，如古代杂交和多倍体发挥重要作用的竹子。BDG复合体的四个属具有复杂的进化历史，这可能是古代渗入事件的产物。
The Bambusa-Dendrocalamus-Gigantochloa complex (BDG complex) is the most diversified and phylogenetically recalcitrant group of the paleotropical woody bamboos. Species of this complex occur in tropical and subtropical Asia and most of them are of great economic, cultural and ecological value. The lack of resolution achieved through the analyses of previous molecular datasets has long confounded its phylogenetic estimation and generic delimitation. Here, we adopted a ddRAD-seq strategy to investigate phylogenetic relationships of the four main genera (Bambusa, Dendrocalamus, Gigantochloa, and Melocalamus) in the BDG complex. A total of 102 species were sampled, and SNP data were generated. Both MP and ML analyses of the ddRAD-seq data resulted in a well-resolved topology with Gigantochloa and Melocalamus confirmed as monophyletic, and Melocalamus resolved as sister to the rest of the complex. Bambusa and Dendrocalamus were both resolved as paraphyletic. The phylogenetic relationships were mostly supported by morphological evidence including characters of the branch complement, rachilla, lodicules, filaments and stigma. We also generated and assembled complete plastid genomes of 48 representative species. There were conflicts between the plastome and the ddRAD topologies. Our study demonstrated that RAD-seq can be used to reconstruct evolutionary history of lineages such as the bamboos where ancient hybridization and polyploidy play a significant role. The four genera of the BDG complex have a complex evolutionary history which is likely a product of ancient introgression events.